Natural minerals in soil can inhibit the growth of bacteria that protect organic carbon from decay. However, the mechanism inhibiting the bacterial growth remains poorly understood. Here, using a series of cultivation experiments and biological, chemical and synchrotron-based spectral analyses, we showed that kaolinite, hematite, goethite and ferrihydrite had a significant inhibitory effect on the growth of the model bacteria Pseudomonas brassicacearum J12, which was more prominent with a concentration of 25 mg mL−1 than it was with either 10 or 5 mg mL−1. In contrast, montmorillonite promoted the growth of J12. Compared to Al-containing minerals, Fe(III)-containing minerals produced more hydroxyl radical (HO⚫) that has high efficiency for the inhibition of J12. Moreover, a significant positive correlation between HO⚫ radical and Fe(II) was found, suggesting that Fe(II) contributes to the generation of HO⚫. Furthermore, both micro X-ray fluorescence and X-ray photoelectron spectroscopies indicated that surface Fe(III) was reduced to Fe(II), which can produce HO⚫ through the well-known Fenton reaction series. Together, these findings indicate that the reduced surface Fe(II) derived from Fe(III)-containing minerals inhibits the growth of Pseudomonas brassicacearum J12 via a free-radical mechanism, which may serve as a ubiquitous mechanism between iron minerals and all of the heterotrophic bacteria in view of taxonomically and ecologically diverse heterotrophic bacteria from terrestrial environments as a vast source of superoxide.